Zinc in PDB 1hzx: Crystal Structure of Bovine Rhodopsin

The structure of Crystal Structure of Bovine Rhodopsin, PDB code: 1hzx was solved by D.C.Teller, T.Okada, C.A.Behnke, K.Palczewski, R.E.Stenkamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	97.246, 97.246, 149.544, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.2

The structure of Crystal Structure of Bovine Rhodopsin also contains other interesting chemical elements:

Mercury

(Hg)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of Bovine Rhodopsin (pdb code 1hzx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Bovine Rhodopsin, PDB code: 1hzx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn957 b:65.0 occ:0.50 NE2 A:GLN279 2.0 45.2 1.0 OE2 A:GLU201 2.1 51.9 1.0 CD A:GLN279 2.7 45.8 1.0 OE1 A:GLN279 2.9 47.5 1.0 CD A:GLU201 3.0 50.8 1.0 CG A:GLU201 3.3 49.0 1.0 CE1 A:PHE276 3.7 34.6 1.0 O A:PHE276 3.9 44.9 1.0 CG A:GLN279 4.1 44.6 1.0 CD1 A:PHE276 4.1 36.1 1.0 OE1 A:GLU201 4.2 51.1 1.0 CZ A:PHE276 4.4 32.9 1.0 CA A:PRO194 4.6 39.5 1.0 CB A:GLU201 4.7 48.7 1.0 CG A:PRO194 4.7 38.8 1.0 CB A:PRO194 4.8 38.3 1.0 O A:TYR191 4.8 36.6 1.0 N A:PRO194 5.0 38.7 1.0 C A:PHE276 5.0 43.5 1.0

Zinc binding site 2 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn959 b:39.5 occ:1.00 CA A:GLY329 2.6 74.4 1.0 NZ A:LYS311 3.0 41.6 1.0 CE1 B:HIS100 3.2 36.0 1.0 NH2 A:ARG314 3.3 30.5 1.0 N A:GLY329 3.5 72.4 1.0 NE2 B:HIS100 3.5 37.2 1.0 N A:ASP330 3.5 76.3 1.0 C A:GLY329 3.5 75.8 1.0 ND2 A:ASN315 3.6 42.5 1.0 CE A:LYS311 3.8 42.9 1.0 NE A:ARG314 3.8 30.4 1.0 O A:LEU328 3.9 69.2 1.0 CZ A:ARG314 4.0 28.7 1.0 C A:LEU328 4.0 71.1 1.0 OD1 A:ASN315 4.0 42.8 1.0 CG A:ASN315 4.2 41.7 1.0 O A:PRO327 4.3 73.0 1.0 ND1 B:HIS100 4.3 34.1 1.0 CG A:LYS311 4.4 43.4 1.0 OH B:TYR96 4.4 66.4 1.0 O A:GLY329 4.7 76.5 1.0 CD A:LYS311 4.7 43.6 1.0 CE2 B:TYR96 4.7 60.4 1.0 CZ B:TYR96 4.8 63.3 1.0 CD2 B:HIS100 4.8 36.5 1.0 CA A:ASP330 4.9 76.0 1.0

Zinc binding site 3 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn962 b:47.8 occ:0.50 ND1 A:HIS211 2.2 35.3 1.0 O A:MET163 2.6 28.7 1.0 NE1 A:TRP126 2.7 35.4 1.0 CE1 A:HIS211 2.7 36.2 1.0 CB A:CYS167 2.7 25.3 1.0 OE1 A:GLU122 2.9 30.9 1.0 CG A:HIS211 3.1 34.9 1.0 CD A:GLU122 3.3 31.6 1.0 CG A:GLU122 3.3 31.8 1.0 C A:MET163 3.4 29.0 1.0 CD1 A:TRP126 3.5 34.5 1.0 NE2 A:HIS211 3.6 36.0 1.0 CA A:ALA164 3.6 27.2 1.0 CB A:GLU122 3.6 29.7 1.0 N A:CYS167 3.7 27.8 1.0 O A:ALA164 3.8 23.5 1.0 CB A:HIS211 3.8 34.8 1.0 CE2 A:TRP126 3.8 35.2 1.0 CA A:CYS167 3.8 25.8 1.0 CD2 A:HIS211 3.8 35.9 1.0 N A:ALA164 3.8 28.3 1.0 SG A:CYS167 3.9 25.3 1.0 C A:ALA164 4.0 25.6 1.0 CZ2 A:TRP126 4.2 34.5 1.0 OE2 A:GLU122 4.3 32.5 1.0 CA A:MET163 4.5 30.6 1.0 CA A:HIS211 4.7 34.4 1.0 C A:ALA166 4.7 28.8 1.0 CB A:MET163 4.7 32.7 1.0 CG A:TRP126 4.8 32.3 1.0 CA A:GLU122 4.9 27.8 1.0 CB A:ALA164 4.9 29.2 1.0 C A:CYS167 4.9 25.1 1.0 CD2 A:TRP126 4.9 33.8 1.0

Zinc binding site 4 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn964 b:46.9 occ:0.50 CG A:PRO267 2.3 24.4 1.0 N A:TYR268 2.5 31.3 1.0 CB A:TYR268 3.1 32.6 1.0 CD A:PRO267 3.1 22.8 1.0 CB A:PRO267 3.2 24.9 1.0 CA A:TYR268 3.3 31.6 1.0 O A:CYS264 3.3 24.8 1.0 O A:PRO291 3.3 15.1 1.0 C A:PRO267 3.4 29.1 1.0 N A:PRO267 3.6 23.5 1.0 CA A:PRO267 3.6 26.1 1.0 C A:CYS264 3.8 24.0 1.0 C A:TRP265 3.8 22.7 1.0 CB A:PRO291 3.8 13.6 1.0 CA A:TRP265 3.9 22.2 1.0 O A:TRP265 3.9 22.3 1.0 C A:PRO291 4.0 15.0 1.0 CA A:PRO291 4.0 14.2 1.0 CD2 A:PHE294 4.0 18.9 1.0 N A:TRP265 4.1 22.7 1.0 CB A:ALA295 4.2 15.8 1.0 O A:ILE263 4.3 25.2 1.0 C A:LEU266 4.4 22.4 1.0 N A:LEU266 4.4 23.0 1.0 CE2 A:PHE294 4.4 17.1 1.0 O A:PRO267 4.4 29.7 1.0 CG A:TYR268 4.5 33.0 1.0 C A:TYR268 4.6 30.3 1.0 CA A:ALA295 4.7 18.5 1.0 N A:ALA295 4.8 17.8 1.0 CA A:CYS264 4.8 24.3 1.0 N A:ALA269 4.9 30.2 1.0

Zinc binding site 5 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn956 b:65.2 occ:0.50 NE2 B:HIS195 3.0 56.9 1.0 O B:PRO7 3.0 42.9 1.0 CE1 B:HIS195 3.6 56.4 1.0 CB B:PRO7 3.7 37.6 1.0 CA B:PRO7 3.7 38.4 1.0 C B:PRO7 3.7 40.6 1.0 CD2 B:HIS195 4.1 57.7 1.0 OE1 B:GLU197 4.2 70.3 1.0 NH2 B:ARG177 4.7 32.2 1.0 ND1 B:HIS195 4.7 55.9 1.0 CD B:GLU197 4.7 69.6 1.0 OE2 B:GLU197 4.9 70.2 1.0

Zinc binding site 6 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn958 b:65.2 occ:0.40 NE2 B:GLN279 1.6 49.4 1.0 OE2 B:GLU201 2.5 79.0 1.0 CD B:GLN279 2.7 46.9 1.0 OE1 B:GLN279 3.1 45.6 1.0 CD B:GLU201 3.5 77.0 1.0 O B:PHE276 3.9 33.0 1.0 CG B:GLU201 3.9 74.1 1.0 CG B:GLN279 4.0 46.0 1.0 CG B:PRO194 4.4 51.1 1.0 CE1 B:PHE276 4.5 32.4 1.0 OE1 B:GLU201 4.5 78.5 1.0 CB B:PRO194 4.7 51.5 1.0 CD1 B:PHE276 4.8 31.4 1.0 CA B:PRO194 4.8 50.1 1.0 CB B:GLN279 4.9 45.8 1.0

Zinc binding site 7 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Bovine Rhodopsin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn963 b:53.8 occ:0.50 ND1 B:HIS211 2.2 45.8 1.0 NE1 B:TRP126 2.5 55.8 1.0 O B:MET163 2.6 49.8 1.0 CE1 B:HIS211 2.6 46.5 1.0 CB B:CYS167 2.8 43.9 1.0 OE1 B:GLU122 3.0 43.2 1.0 CG B:HIS211 3.1 45.3 1.0 C B:MET163 3.3 48.2 1.0 CD1 B:TRP126 3.4 55.3 1.0 CD B:GLU122 3.5 43.0 1.0 CG B:GLU122 3.5 40.6 1.0 NE2 B:HIS211 3.6 46.5 1.0 CE2 B:TRP126 3.6 56.2 1.0 CA B:ALA164 3.6 43.9 1.0 CB B:GLU122 3.7 38.1 1.0 CB B:HIS211 3.7 44.1 1.0 CD2 B:HIS211 3.8 46.8 1.0 N B:ALA164 3.8 46.2 1.0 N B:CYS167 3.8 43.8 1.0 O B:ALA164 3.9 41.7 1.0 CA B:CYS167 3.9 43.0 1.0 SG B:CYS167 4.1 45.7 1.0 CZ2 B:TRP126 4.1 57.1 1.0 C B:ALA164 4.1 42.3 1.0 CA B:MET163 4.4 48.5 1.0 OE2 B:GLU122 4.4 43.9 1.0 CB B:MET163 4.6 50.1 1.0 CG B:TRP126 4.6 53.6 1.0 CA B:HIS211 4.6 43.4 1.0 CD2 B:TRP126 4.7 55.3 1.0 C B:ALA166 4.8 43.7 1.0 CB B:ALA164 4.9 43.2 1.0 CA B:GLU122 4.9 36.1 1.0 CB B:ALA166 5.0 42.4 1.0

D.C.Teller, T.Okada, C.A.Behnke, K.Palczewski, R.E.Stenkamp. Advances in Determination of A High-Resolution Three-Dimensional Structure of Rhodopsin, A Model of G-Protein-Coupled Receptors (Gpcrs). Biochemistry V. 40 7761 2001.
ISSN: ISSN 0006-2960
PubMed: 11425302
DOI: 10.1021/BI0155091